Over the next few years, the el-Hage family travelled repeatedly to Pakistan, initially taking along his mother-in-law and her husband. In an interview with PBS Frontline, el-Hage's mother-in-law said, "I was the matron surgical nurse at an Afghan surgical hospital. Wadih did not actually fight, but acted as an educator. My husband went with Wadih to deliver textbooks and Qur'ans to the young people. It was a Jihad, a fight for Islam."

Prosecutors have also suggested that el-Hage and Jamaat ul-Fuqra were involved in the murder of Dr. Rashad Khalifa on January 31, 1990 in Tucson. They believe that el-Hage knows who killed Khalifa. And even if el-Hage was not himself involved, the prosecution asked why he had not told them what he knew. El-Hage's family says he was not in the country at the time of the murder.

At some later point el-Hage moved with his family to Arlington, Texas. He was called to the Brooklyn charity Alkifah Refugee Center, by the group's office in Tucson, via el-Hage's mosque in Arlington. Family members acknowledge that he was in contact with the Alkifah group, and say that he was called in to mediate a dispute. A week later, the group's leader Mustafa Shalabi was found stabbed to death in an apartment that he shared with Abouhalima. This murder is unsolved. El-Hage's family said that he cried when he heard that Shalabi was dead.

Shortly thereafter, el-Hage moved his family to Sudan and worked as a secretary for Osama bin Laden, who operated a network of businesses and charities, some of them fronts, in East Africa at the time. El-Hage often travelled to Europe in this capacity. Prosecutors believe that el-Hage became a key aide to Bin Laden. They also believe that he was trying to obtain chemical weapons for the terrorist group. Little public evidence has emerged from Sudan for these claims.

In 1994, his wife April convinced el-Hage to leave Sudan and stop working for Bin Laden's organization there. As his mother in law said, "April would have none of that. She is Muslim, but she is also American, and she wouldn't stand for it." But prosecutors believe that el-Hage continued to work for bin Ladin's organisation in Nairobi, Kenya. In Kenya, he became the director of Help Africa People, a Muslim charity organization, which Kenyan documents say helped control malaria. El-Hage also made money off in the jewelry business. Prosecutors say that el-Hage was in contact in Kenya with Abu Ubaidah al-Banshiri, who was al-Qaeda's #2 member until his death in 1996. The badly wanted al-Qaeda suspect Fazul Abdullah Mohammed moved in and worked at the house as a secretary. A letter,[8] thought to be from Mohammed, suggests el-Hage was the "engineer" of this East African cell. Yet another al-Qaeda member, Mohammed Saddiq Odeh admitted knowing el-Hage in Nairobi, and said that el-Hage attended his wedding.

Mamoun Darkazanli, Syrian-born businessman living in Hamburg, Germany, who had contacts with Mohamed Atta’s al-Qaeda cell in the same city. Darkazanli’s name and phone number are listed, and el-Hage even has a business card listing el-Hage’s address in Texas and Darkazanli’s address in Hamburg.

Ghassan Dahduli, an associate of el-Hage's from Tucson, AZ. Dahduli was affiliated with the Illinois-based Islamic Association for Palestine, suspect at one time of being a Hamas front organization, and the commercial web-hosting service InfoCom Corporation which would later be raided by the US Joint Terrorism Task Force. Though Dahduli himself is apparently quite innocuous, the INS would have him deported to Jordan in late 2001.[10]

El-Hage himself was questioned two days later upon his return to Nairobi from Afghanistan. El-Hage's family says that he was told to leave Kenya. In September 1998 he returned to Arlington with his family; several accounts say that he sold all of his possessions to fund the trip. However, upon arriving in the United States, he was arrested on September 15, 1998.[11]

Before a Grand Jury, el-Hage denied knowing bin Laden and others accused of the embassy bombings. On 20 September he was arrested for perjury, and has not been free since. The indictment for the bombings themselves was read on 7 October of that year.